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Objectives To determine the age- and sex-specific differences of physical fitness performances and Body Mass Index (BMI) in basic training and the operational Army. Design Cross-sectional Study. Methods This secondary analysis utilizes retrospective surveys of U.S. Army Soldiers in Basic Combat Training (BCT) and operational units to compare physical performances between men and women as measured by the Army Physical Readiness Test (APFT). An ANOVA was used to compare mean differences in APFT results and BMI within sex-specific populations. A post hoc Tukey test identified specific mean differences. Adjusting for age, an ANCOVA was used to compare sex and occupation (infantry and non-infantry) differences in APFT results. Results Surveyed populations consisted of 2216 BCT Soldiers (1573 men and 643 women) and 5515 Operational Soldiers (4987 men and 528 women). Male and female operational Soldiers had greater muscular performance (79%–125% higher APFT push-ups, 66%–85% higher APFT sit-ups) and cardiorespiratory performance (22%–24% faster APFT 2-mile run times) than BCT Soldiers. Male BCT and operational Soldiers outperform their female counterparts on tests of muscular and cardiorespiratory endurance. Sex differences in physical performances attenuated among female Soldiers in operational units compared to BCT. Among male operational Soldiers, infantry Soldiers exhibited greater cardiorespiratory and muscular performance than non-infantry Soldiers. Higher BMI was associated with higher age groups, except for female BCT Soldiers. Conclusions Gaps in cardiorespiratory and muscular performances between men and women should be addressed through targeted physical training programs that aim to minimize physiological differences.